Current build/Steam/Windows 10
Basically, the Crossbowman doesn’t get replaced after sending “Scharnhorst Reform”, the Crossbowman icon remains but grayed out, “only trainable in Age II”.
It’s the only military building with this issue, and it can’t be intended behaviour (like let’s say only archaic infantry can be trained) cause Skirmishers are trainable.
This applies to both the regular Citadel sent from a Maya settlement and the special version on Unknown that can train villagers.
Oh, and it can be reproduced, it’s always the case.